Why study synthesis?
revtools
#EShackathon
Future directions
Outline
Scientific learning can be translated into tangible benefits
for society and the environment
Westgate et al. (2018) Sofware support for environmental evidence synthesis.
Nature Ecology & Evolution 2(4): 588
Data from: MJ Westgate, AIT Tulloch, PS Barton, JC Pierson & DB Lindenmayer (2017)
Optimal taxonomic groups for biodiversity assessment: a meta-analytic approach.
Ecography 40: 539-548
Scientific learning can be translated into tangible benefits
for society and the environment
…but this requires synthesis
Westgate et al. (2018) Sofware support for environmental evidence synthesis.
Nature Ecology & Evolution 2(4): 588
L Bormann & R Mutz (2015) Growth rates of modern science:
A bibliometric analysis based on the number of publications and cited references.
JAIST 66(11): 2215-2222
NR Haddaway & MJ Westgate (in review)
A tool for predicting the time taken to conduct an environmental systematic review
A tool for predicting the time taken to conduct an environmental systematic review
- standardised import of multiple formats
- flexible de-duplication
- interactive visualisation and article selection
library(revtools) # load
data <- read_bibliography("data/Westgate_scopus_2018_04.ris") # import
summary(data)
## label type author ## Length:25 Length:25 Length:25 ## Class :character Class :character Class :character ## Mode :character Mode :character Mode :character ## year title journal ## Length:25 Length:25 Length:25 ## Class :character Class :character Class :character ## Mode :character Mode :character Mode :character ## volume issue pages ## Length:25 Length:25 Length:25 ## Class :character Class :character Class :character ## Mode :character Mode :character Mode :character ## abstract doi url ## Length:25 Length:25 Length:25 ## Class :character Class :character Class :character ## Mode :character Mode :character Mode :character ## address keywords ## Length:25 Length:25 ## Class :character Class :character ## Mode :character Mode :character
print(data[1])
## label ## 1 Westgate_2018_NatEcoandEvo ## 2 Westgate_2018_DivandDis ## 3 Westgate_2017_ConsBiol ## 4 Westgate_2017_Ecog ## 5 Tulloch_2016_Ecog ## 6 Lindenmayer_2016_BiolCons ## 7 Lindenmayer_2016_EcolAppl ## 8 Hunter_2016_EcolIndi ## 9 Lindenmayer_2015_ScofthToEn ## 10 Westgate_2015_ConsBiol ## 11 Westgate_2015_PLoONE ## 12 Mortelliti_2015_BasandAppEco ## 13 Barton_2015_Oiko ## 14 Stojanovic_2015_JoofAnEc ## 15 Westgate_2014_NatuComm ## 16 Driscoll_2014_PLoONE ## 17 Lindenmayer_2014_PLoONE ## 18 Mortelliti_2014_JoofApEc ## 19 Lane_2014_EcoandEvo ## 20 Barton_2014_JoofApEc ## 21 Lindenmayer_2014_ConsBiol ## 22 Westgate_2013_BiolCons ## 23 Westgate_2012_Oiko ## 24 Westgate_2012_BiolCons ## 25 Felton_2009_BioandCon
data <- read_bibliography("data/Westgate_scopus_2018_04.ris")
str(as.data.frame(data))
## 'data.frame': 25 obs. of 14 variables: ## $ label : chr "Westgate_2018_NatEcoandEvo" "Westgate_2018_DivandDis" "Westgate_2017_ConsBiol" "Westgate_2017_Ecog" ... ## $ type : chr "JOUR" "JOUR" "JOUR" "JOUR" ... ## $ author : chr "Westgate, M.J. and Haddaway, N.R. and Cheng, S.H. and McIntosh, E.J. and Marshall, C. and Lindenmayer, D.B." "Westgate, M.J. and MacGregor, C. and Scheele, B.C. and Driscoll, D.A. and Lindenmayer, D.B." "Westgate, M.J. and Lindenmayer, D.B." "Westgate, M.J. and Tulloch, A.I.T. and Barton, P.S. and Pierson, J.C. and Lindenmayer, D.B." ... ## $ year : chr "2018" "2018" "2017" "2017" ... ## $ title : chr "Software support for environmental evidence synthesis" "Effects of time since fire on frog occurrence are altered by isolation, vegetation and fire frequency gradients" "The difficulties of systematic reviews" "Optimal taxonomic groups for biodiversity assessment a meta-analytic approach" ... ## $ journal : chr "Nature Ecology and Evolution" "Diversity and Distributions" "Conservation Biology" "Ecography" ... ## $ volume : chr "2" "24" "31" "40" ... ## $ issue : chr "4" "1" "5" "4" ... ## $ pages : chr "588-590" "82-91" "1002-1007" "539-548" ... ## $ abstract: chr "Evidence-based environmental management is being hindered by difficulties in locating, interpreting and synthes"| __truncated__ "Aim To quantify how frogs in terrestrial environments respond to recurrent fire, and to what extent this is med"| __truncated__ "The need for robust evidence to support conservation actions has driven the adoption of systematic approaches t"| __truncated__ "A fundamental decision in biodiversity assessment is the selection of one or more study taxa, a choice that is "| __truncated__ ... ## $ doi : chr "10.1038/s41559-018-0502-x" "10.1111/ddi.12659" "10.1111/cobi.12890" "10.1111/ecog.02318" ... ## $ url : chr "https//www.scopus.com/inward/record.uri?eid=2-s2.0-85044402000&doi=10.1038%2fs41559-018-0502-x&partnerID=40&md5"| __truncated__ "https//www.scopus.com/inward/record.uri?eid=2-s2.0-85037556950&doi=10.1111%2fddi.12659&partnerID=40&md5=bd03c28"| __truncated__ "https//www.scopus.com/inward/record.uri?eid=2-s2.0-85021013390&doi=10.1111%2fcobi.12890&partnerID=40&md5=131a71"| __truncated__ "https//www.scopus.com/inward/record.uri?eid=2-s2.0-84963987432&doi=10.1111%2fecog.02318&partnerID=40&md5=ace38b"| __truncated__ ... ## $ address : chr "Fenner School of Environment and Society, Australian National University, A-Acton, ACT, Australia and Mistra Ev"| __truncated__ "Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia and Long"| __truncated__ "Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia and ARC "| __truncated__ "The Fenner School of Environment and Society, The Australian National Univ., Canberra, ACT, Australia" ... ## $ keywords: chr NA "amphibians and disturbance and fire regime and pyrodiversity" "anlisis de texto and bias and margen de error and meta-analysis and meta-anlisis and sinonimia and synonymy and"| __truncated__ NA ...
Where next?
- Utility: Is revtools useful for real tasks?
- Validation: Does it provide useful, unbiased information?
- User experience: Can revtools be optimised to increase speed and reduce fatigue?
- Outcomes: Does it lead to better, more accurate reviews?
And yet…
- Not everyone in ES uses code
- Some problems not suited to R (e.g. better searching)
- Some questions are fiddly but conceptually simple
#ESHackathon
Hackathon goals:
- Fill software gaps to make evidence synthesis more efficient
- Increase access to high quality tools (open source)
- Improve networks linking researchers, users and developers
New software:
- Search
- Paperweight: Natural language processing for improved search queries
- KeywordX: A search strategy support tool
- ROSES (RepOrting standards for Systematic Evidence Syntheses): website overhaul
- Data extraction
- PDF annotation and data coding/extraction tool
- A tool to extract reference lists from PDFs
- A tool to fill in missing information from incomplete references
- Presentation
- A function for dynamically generating analysis reports based on model outputs within metafor
- EviAtlas: An R Shiny app for plotting outcomes from systematic maps
- Thalloo Evidence-Mapping: A Jekyll theme for visualisation of datasets
Future directions
- Working with participants to develop & promote their software
- Planning #ESHackathon 2019 (Australia?)
- Selective mapping of the ES software universe
- Search options
- R packages
- see also http://systematicreviewtools.com
Summary
- Existing software can make ES projects easier
- We are expanding, mapping and testing this software
- Next 2-3 years will see large changes in ES methodology
- Major challenges are in integration and cultural change
~ collaborators ~
Neal Haddaway - David Lindenmayer - Shinichi Nakagawa
~ ESHackathon ~
Marc Lajeunesse - Wolfgang Viechtbauer - Laurie Baker - Sergio Leonardo Benitez Diaz
Panagiotis Bozelos - Katie Corker - Brian Cottrell - Sanita Dhaubanjar - Spencer Dixon
Jacqui Eales - Andrew Feierman - Matt Grainger - Charles Gray - Sarah Han - Udit Jain - Peter Ma
Biljana Macura - Andrew Martin - Geoffrey Martin - Sonia Mitchell - Christopher Penkin - Daniel Perez
Gihan Samarasinghe - Gorm Shackelford - Mridul Shrestha - Ezgi Tanriver-Ayder - Juan Vasquez
~ funding ~
Ecological Society of Australia - Fenner School - Stockholm Environment Institute
ARC Centre of Excellence for Environmental Decisions
~ revtools ~
website - https://revtools.net
download - https://CRAN.R-project.org/package=revtools
source - https://github.com/mjwestgate/revtools
~ this presentation was created using R ~
rmarkdown - revtools - plotly - ggridges - treemap - viridis
~ contact ~
martin.westgate@anu.edu.au - @westgatecology